6NIL | pdb_00006nil

cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex

• PDB DOI: https://doi.org/10.2210/pdb6NIL/pdb
• EM Map EMD-9380: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-12-29 Released: 2019-12-11 
• Deposition Author(s): Hu, Y., Xiong, Y.
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of antagonism of human APOBEC3F by HIV-1 Vif.

Hu, Y., Desimmie, B.A., Nguyen, H.C., Ziegler, S.J., Cheng, T.C., Chen, J., Wang, J., Wang, H., Zhang, K., Pathak, V.K., Xiong, Y.

(2019) Nat Struct Mol Biol 26: 1176-1183

• PubMed: 31792451 
• DOI: https://doi.org/10.1038/s41594-019-0343-6
• Primary Citation Related Structures: 
  6NIL


• PubMed Abstract: 
  

  HIV-1 virion infectivity factor (Vif) promotes degradation of the antiviral APOBEC3 (A3) proteins through the host ubiquitin-proteasome pathway to enable viral immune evasion. Disrupting Vif-A3 interactions to reinstate the A3-catalyzed suppression of human immunodeficiency virus type 1 (HIV-1) replication is a potential approach for antiviral therapeutics. However, the molecular mechanisms by which Vif recognizes A3 proteins remain elusive. Here we report a cryo-EM structure of the Vif-targeted C-terminal domain of human A3F in complex with HIV-1 Vif and the cellular cofactor core-binding factor beta (CBFβ) at 3.9-Å resolution. The structure shows that Vif and CBFβ form a platform to recruit A3F, revealing a direct A3F-recruiting role of CBFβ beyond Vif stabilization, and captures multiple independent A3F-Vif interfaces. Together with our biochemical and cellular studies, our structural findings establish the molecular determinants that are critical for Vif-mediated neutralization of A3F and provide a comprehensive framework of how HIV-1 Vif hijacks the host protein degradation machinery to counteract viral restriction by A3F.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
IGBMC, CNRS, Illkirch, France.
School of Life Sciences, Tsinghua University, Haidian District, Beijing, China.
Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA. [e-mail].
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 236.34 kDa 
• Atom Count: 15,220 
• Modeled Residue Count: 1,800 
• Deposited Residue Count: 1,984 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA dC->dU-editing enzyme APOBEC-3F	A, D, G, J	207	Homo sapiens	Mutation(s): 10  Gene Names: APOBEC3F EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUX4 (Homo sapiens) Explore Q8IUX4  Go to UniProtKB:  Q8IUX4
PHAROS:  Q8IUX4 GTEx:  ENSG00000128394

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Core-binding factor subunit beta	B, E, H, K	151	Homo sapiens	Mutation(s): 0  Gene Names: CBFB
UniProt & NIH Common Fund Data Resources
Find proteins for Q13951 (Homo sapiens) Explore Q13951  Go to UniProtKB:  Q13951
PHAROS:  Q13951 GTEx:  ENSG00000067955

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion infectivity factor	C, F, I, L	138	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: vif
UniProt
Find proteins for P12504 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12504  Go to UniProtKB:  P12504

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	M [auth A], N [auth D], O [auth G], P [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Hu, Y., Xiong, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	AI116313

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence, Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references